Aims: Microcystis population and microcystin (MC) dynamics were investigated in western Lake Erie coastal wetlands and downstream beach water. A three-dimensional (3-D) model was developed to quantify how Microcystis population size and structure affect MCs. Methods and Results: Real-time PCR, denaturing gradient gel electrophoresis (DGGE) and enzyme-linked immunoabsorbent assay (ELISA) were used. A moderate-low level of Microcystis abundance and MCs were detected with a significant increase along the wetland flow and the spatiotemporal homogeneity of Microcystis populations. The proportion of toxigenic and nontoxgenic genotypes appeared to be more affected by the variation in two major Microcystis PC-IGS genotypes. MC dynamics was associated with the changing Microcystis population size and structure. The 3-D model showed that Microcystis population with greater Microcystis PC-IGS abundance (and simultaneously higher diversity) had more MCs. Conclusion: Microcystin variation was significantly affected by Microcystis population size and structure. The 3-D model also revealed the relative importance of Microcystis population size and structure in determining MCs in the Lake Erie costal wetland and downstream beach water. Significance and Impact of the Study: This study enriches our understanding of Microcystis population and microcystin ecology in a western Lake Erie coastal wetland and downstream beach water. Our illustrative model brings a new perspective for understanding the ecological relationship between Microcystis population size and structure and MCs.